This research will identify and model the biological and physical mechanisms regulating two key processes in the blooms of Alexandrium dinoflagellates responsible for paralytic shellfish poisoning (PSP): bloom initiation and termination. A key feature of the project is that it will be conducted in the Nauset Marsh System (NMS), a shallow estuary that has recurrent A. fundyense blooms in its three terminal kettie ponds, with blooms being unequivocally tied to cyst seedbeds in those embayments. The NMS represents a natural mesocosm where these processes can be studied in a manner not possible in open coastal waters. The NMS also represents a major habitat for toxic Alexandrium species in the US and worldwide. Aim 1 comprises field and lab experiments on bloom initiation. Excystment experiments will determine whether internal or external factors regulate germination seasonality, and other studies will measure the effects of temperature, salinity, and light on germination and growth. The timing and rate of escape of germinated cells will be measured using plankton emergence traps, and high-resolution sampling will be conducted throughout bloom initiation. Aim 2 activities are focused on bloom termination. A unique submersible flow cytometer with imaging capabilities (the imaging flow cytobot, IFCB) will detect life cycle transitions in situ. Routine and adaptive field sampling (triggered by IFCB data) will document factors associated with life cycle transitions, and sediment traps will assess the timing and rate of cyst deposition. Complimentary efforts will utilize a bentop multi-daser IFCB to confirm the presence of sexual forms in field samples, an assessment of the linkage between A. fundyense encystment and parasite infection, and the development of biomarker assays for detection of gametes and planozygotes that will be applied in sampling for these stages in situ. In Aim 3, an innovative Lagrangian approach will model Alexandrium population dynamics within the NMS, including life cycle transitions. The model will be formulated and calibrated against blooms in the NMS, but is broadly transferable to HAB models in estuarine or coastal settings, including Project 2 in this program.